OxoScan - Figure 3 + 4

COVID-19 glycoproteomic analysis with OxoScan

 

 

Import OxoScan output for COVID-19 cohort

## [1] "1102 glycopeptide features called and quantified across Kuebler cohort"

 

 

OxoScan output table:

 

 

Normalised sample intensities across 162 injection cohort (Figure 4b)  

 

 

Variation in instrument (MS), whole process (SP) and clinical samples (Figure 4c)

 

 

Checkpoint - peaks quantified by OxoScan across cohort:

## [1] "1002 features taken forward following interference filtering"

## [1] "567 features quantified robustly (median CV < 20%) across clinical cohort"

## [1] "99.43% of features with retention time shift below 12s"

 

 

Differential expression analysis (Supplementary Figure)

## [1] "230 differentially expressed features (Severe/Healthy) - |logFC| > 1, p.adj < 0.05"

 

 

Principal Component Analysis of COVID-19 Glycoproteomes (Figure 4e)

 

 

Hierarchical Clustering by Glycoproteome

 

 

Matching DDA-identified glycopeptides to OxoScan-quantified features

 

 

Identifying glycopeptide precursors with MS1/Q1 overlay spectra, back-to-back CID/HCD spectra comparison and OxoScan quantification for each feature

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RT comparison of matched glycopeptides between microflow (DIA) and nanoflow (DDA) platforms (Supp. Figure X)

 

 

Dynamic range of quantified features in COVID-19 cohort (Figure 4d)

 

 

Glycopeptide-specific abundance changes in response to COVID-19 severity (Figure 4g)